|
||||||||||
| PREV NEXT | FRAMES NO FRAMES | |||||||||
ADHOC_TAGSETS_PARAM='a'
ANALYSIS_VIEW="redirect:/myAnalisysList.htm"
AND=4
AND=4
AUTOFLUSH=false
BadFile=3
BadModule=4
BadParameter=2
BadRunnerParams=5
BATCH_SIZE=100000
BATCH_SIZE_PARAM='b'
BENCHMARKING_BATCH_SIZE=20000
BENCHMARKING_BATCH_SIZE=20000
BRACKET_CLOSE=5
BRACKET_CLOSE=5
BRACKET_OPEN=6
BRACKET_OPEN=6
BUFFERSIZE=500*1024
BYTEA=1
BYTEA=1
BYTEA=1
CHECK="check"
CHECK="check"
COMMENT_EOL=7
COMMENT_EOL=7
COMMENT_INLINE=8
COMMENT_INLINE=8
COMPLETED="completed"
COMPRESSED_PARAM='c'
CONSEQUENCE=60
CONST_AT_SIGN="@"
CONTIGPOSITION=50
COVERAGE=40
JAXBElement<AnalysisType>}
AnalysisSet
AnalysisType
AnalysisType.ANALYSISATTRIBUTES
AnalysisType.ANALYSISATTRIBUTES.ANALYSISATTRIBUTE
AnalysisType.ANALYSISFILES
AnalysisType.ANALYSISFILES.FILE
AnalysisType.ANALYSISLINKS
AnalysisType.ANALYSISLINKS.ANALYSISLINK
AnalysisType.ANALYSISLINKS.ANALYSISLINK.ENTREZLINK
AnalysisType.ANALYSISLINKS.ANALYSISLINK.URLLINK
AnalysisType.ANALYSISLINKS.ANALYSISLINK.XREFLINK
AnalysisType.ANALYSISTYPE
AnalysisType.PARENT
AnalysisType.PARENT.EXPERIMENTREF
AnalysisType.PARENT.RUNREF
AnalysisType.PARENT.SAMPLEPOOLREF
AnalysisType.PARENT.SAMPLEPOOLREF.MEMBER
AnalysisType.PARENT.SAMPLEREF
AnalysisType.PARENT.STUDYREF
JAXBElement<ExperimentType>}
ExperimentSet
ExperimentType
ExperimentType.DESIGN
ExperimentType.DESIGN.LIBRARYDESCRIPTOR
ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT
ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT.PAIRED
ExperimentType.DESIGN.SAMPLEDESCRIPTOR
ExperimentType.DESIGN.SPOTDESCRIPTOR
ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC
ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
ExperimentType.EXPERIMENTATTRIBUTES
ExperimentType.EXPERIMENTATTRIBUTES.EXPERIMENTATTRIBUTE
ExperimentType.EXPERIMENTLINKS
ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK
ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.ENTREZLINK
ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.URLLINK
ExperimentType.PLATFORM
ExperimentType.PLATFORM.ABISOLID
ExperimentType.PLATFORM.ABISOLID.COLORMATRIX
ExperimentType.PLATFORM.ABISOLID.COLORMATRIX.COLOR
ExperimentType.PLATFORM.HELICOS
ExperimentType.PLATFORM.ILLUMINA
ExperimentType.PLATFORM.LS454
ExperimentType.PROCESSING
ExperimentType.PROCESSING.BASECALLS
ExperimentType.PROCESSING.QUALITYSCORES
ExperimentType.STUDYREF
JAXBElement<RunType>}
RunSet
RunType
RunType.DATABLOCK
RunType.DATABLOCK.FILES
RunType.DATABLOCK.FILES.FILE
RunType.EXPERIMENTREF
RunType.RUNATTRIBUTES
RunType.RUNATTRIBUTES.RUNATTRIBUTE
RunType.RUNLINKS
RunType.RUNLINKS.RUNLINK
RunType.RUNLINKS.RUNLINK.ENTREZLINK
RunType.RUNLINKS.RUNLINK.URLLINK
JAXBElement<SampleType>}
SampleSet
SampleType
SampleType.MEMBERS
SampleType.MEMBERS.MEMBER
SampleType.SAMPLEATTRIBUTES
SampleType.SAMPLEATTRIBUTES.SAMPLEATTRIBUTE
SampleType.SAMPLELINKS
SampleType.SAMPLELINKS.SAMPLELINK
SampleType.SAMPLELINKS.SAMPLELINK.ENTREZLINK
SampleType.SAMPLELINKS.SAMPLELINK.URLLINK
SampleType.SAMPLENAME
JAXBElement<StudyType>}
StudySet
StudyType
StudyType.DESCRIPTOR
JAXBElement<String>}
StudyType.DESCRIPTOR.STUDYTYPE
StudyType.STUDYATTRIBUTES
StudyType.STUDYATTRIBUTES.STUDYATTRIBUTE
StudyType.STUDYLINKS
StudyType.STUDYLINKS.STUDYLINK
StudyType.STUDYLINKS.STUDYLINK.ENTREZLINK
StudyType.STUDYLINKS.STUDYLINK.URLLINK
JAXBElement<SubmissionType>}
SubmissionSet
SubmissionType
SubmissionType.ACTIONS
SubmissionType.ACTIONS.ACTION
SubmissionType.ACTIONS.ACTION.ADD
SubmissionType.ACTIONS.ACTION.HOLD
SubmissionType.ACTIONS.ACTION.MODIFY
SubmissionType.ACTIONS.ACTION.RELEASE
SubmissionType.ACTIONS.ACTION.SUPPRESS
SubmissionType.ACTIONS.ACTION.VALIDATE
SubmissionType.CONTACTS
SubmissionType.CONTACTS.CONTACT
SubmissionType.FILES
SubmissionType.FILES.FILE
CSV_TYPE="csvtype"
CSV_TYPE="csvtype"
DBCOULDNOTDISCONNECT=81
DBCOULDNOTINITIALIZE=80
DEBUG=true
Category.debug(Object).
Category.debug(Object,Throwable).
DELETION=3
DIRECTORYNOTREADABLE=3
DIRECTORYNOTWRITABLE=11
END_ALL_QUERYDATELONG="end-ALL_query-date-long"
END_PMC_QUERYDATELONG="end-PMC_query-date-long"
END_QUAL_QUERYDATELONG="end-QUAL_query-date-long"
ENVVARNOTFOUND=14
EOF=-1
EOF=-1
EQUALS=9
EQUALS=9
Category.error(Object).
Category.error(Object,Throwable).
EXIT_CODE_EXISTING_NAME=5
EXIT_CODE_INVALID_ARGS=1
EXIT_CODE_INVALID_FILE=10
EXPERIMENT_ATTRIBUTES="Header.EXPERIMENT_ATTRIBUTES.getTitle()"
EXPERIMENT_NAME="Header.EXPERIMENT_NAME.getTitle()"
EXPERIMENT_PREFIX="exp_"
EXPERIMENT_SWA="Header.EXPERIMENT_SWA.getTitle()"
EXPERIMENT_TAG_PREFIX="Header.EXPERIMENT_TAG_PREFIX.getTitle()"
EXT_PARAMETERS="ext_parameters"
FAILED="failed"
FAILED="failed"
FAILED="failed"
FAILED="failed"
FAILURE=15
Category.fatal(Object).
Category.fatal(Object,Throwable).
FEATURE=30
FEATURE_SET_ID="FeatureSetID"
FEATURE_SET_PARAM='f'
FEATURE_SET_PARAM='f'
FIELDS=2
FIELDS=2
FIELDS=2
FILE_EXPERIMENT_NAME="f_exp_name"
FILE_EXPERIMENT_NAME="f_exp_name"
FILE_EXPERIMENT_SWID="f_exp_swid"
FILE_EXPERIMENT_SWID="f_exp_swid"
FILE_FILE="f_file"
FILE_FILE="f_file"
FILE_IUS="f_ius"
FILE_IUS="f_ius"
FILE_IUS_NAME="f_ius_name"
FILE_IUS_SWID="f_ius_swid"
FILE_IUS_SWID="f_ius_swid"
FILE_IUS_TAG="f_ius_tag"
FILE_IUS_TAG="f_ius_tag"
FILE_LANE="f_lane"
FILE_LANE="f_lane"
FILE_LANE_NAME="f_lane_name"
FILE_LANE_NAME="f_lane_name"
FILE_LANE_NUMBER="f_lane_num"
FILE_LANE_NUMBER="f_lane_num"
FILE_LANE_SWID="f_lane_swid"
FILE_LANE_SWID="f_lane_swid"
FILE_LIBRARY="f_library"
FILE_LIBRARY="f_library"
FILE_META_TYPE="f_file_meta"
FILE_META_TYPE="f_file_meta"
FILE_PARENT_SAMPLE_NAME="f_sample_name"
FILE_PARENT_SAMPLE_NAME="f_sample_name"
FILE_PARENT_SAMPLE_SWID="f_sample_swid"
FILE_PARENT_SAMPLE_SWID="f_sample_swid"
FILE_PATH="f_file_path"
FILE_PATH="f_file_path"
FILE_PREFIX="fl_"
FILE_PROCESSING_ALG="f_processing_alg"
FILE_PROCESSING_ALG="f_processing_alg"
FILE_PROCESSING_SWID="f_processing_swid"
FILE_PROCESSING_SWID="f_processing_swid"
FILE_RUN_NAME="f_run_name"
FILE_RUN_NAME="f_run_name"
FILE_RUN_SWID="f_run_swid"
FILE_RUN_SWID="f_run_swid"
FILE_SAMPLE="f_sample"
FILE_SAMPLE="f_sample"
FILE_SAMPLE_NAME="f_child_sample_name"
FILE_SAMPLE_NAME="f_child_sample_name"
FILE_SAMPLE_SWID="f_child_sample_swid"
FILE_SAMPLE_SWID="f_child_sample_swid"
FILE_SEQUENCER_NAME="f_seqrun_name"
FILE_SEQUENCER_NAME="f_seqrun_name"
FILE_SEQUENCER_SWID="f_seqrun_swid"
FILE_SEQUENCER_SWID="f_seqrun_swid"
FILE_STUDY_SWID="f_study_swid"
FILE_STUDY_SWID="f_study_swid"
FILE_STUDY_TITLE="f_study_title"
FILE_STUDY_TITLE="f_study_title"
FILE_SWA="Header.FILE_SWA.getTitle()"
FILE_SWID="f_file_swid"
FILE_SWID="f_file_swid"
FILE_TEMPLATE="f_template"
FILE_TEMPLATE="f_template"
FILE_TISSUE="f_tissue"
FILE_TISSUE="f_tissue"
FILE_WF_NAME="f_wf_name"
FILE_WF_NAME="f_wf_name"
FILE_WF_SWID="f_wf_swid"
FILE_WF_SWID="f_wf_swid"
FILE_WF_VERSION="f_wf_version"
FILE_WF_VERSION="f_wf_version"
FILEEMPTY=12
ValidationReportService.fileLinkReport(List) including all files in the SeqWare
meta db.
ValidationReportService.fileLinkReport(List) including all files in the SeqWare
meta db.
FILENOTEXECUTABLE=10
FILENOTREADABLE=4
FILENOTWRITABLE=5
FILETYPE_ALL="all"
FINISHED="completed"
FLOAT=10
FLOAT=10
FOLLOW_26_in_key_value_function293
FOLLOW_26_in_three_param_predicate342
FOLLOW_26_in_three_param_predicate346
FOLLOW_26_in_two_param_predicate317
FOLLOW_AND_in_high_precedence_constraint117
FOLLOW_BRACKET_CLOSE_in_key_value_function297
FOLLOW_BRACKET_CLOSE_in_nested_constraint145
FOLLOW_BRACKET_CLOSE_in_three_param_predicate350
FOLLOW_BRACKET_CLOSE_in_two_param_predicate321
FOLLOW_BRACKET_OPEN_in_key_value_function288
FOLLOW_BRACKET_OPEN_in_nested_constraint140
FOLLOW_BRACKET_OPEN_in_three_param_predicate337
FOLLOW_BRACKET_OPEN_in_two_param_predicate312
FOLLOW_comparison_in_constraint165
FOLLOW_comparison_in_constraint175
FOLLOW_constant_in_constraint168
FOLLOW_constant_in_constraint173
FOLLOW_constraint_in_nested_constraint151
FOLLOW_EOF_in_query78
FOLLOW_high_precedence_constraint_in_low_precedence_constraint91
FOLLOW_high_precedence_constraint_in_low_precedence_constraint98
FOLLOW_ID_in_identifier200
FOLLOW_identifier_in_constraint163
FOLLOW_identifier_in_constraint178
FOLLOW_key_value_function_in_identifier206
FOLLOW_literal_in_constant249
FOLLOW_literal_in_key_value_function291
FOLLOW_literal_in_key_value_function295
FOLLOW_literal_in_three_param_predicate340
FOLLOW_literal_in_three_param_predicate344
FOLLOW_literal_in_three_param_predicate348
FOLLOW_literal_in_two_param_predicate315
FOLLOW_literal_in_two_param_predicate319
FOLLOW_low_precedence_constraint_in_nested_constraint143
FOLLOW_low_precedence_constraint_in_query75
FOLLOW_NAMED_CONSTANT_in_constant254
FOLLOW_NAMED_FUNCTION_in_key_value_function285
FOLLOW_NAMED_THREE_PARAM_PREDICATE_in_three_param_predicate334
FOLLOW_NAMED_TWO_PARAM_PREDICATE_in_two_param_predicate309
FOLLOW_nested_constraint_in_high_precedence_constraint113
FOLLOW_nested_constraint_in_high_precedence_constraint120
FOLLOW_NOT_in_nested_constraint135
FOLLOW_OR_in_low_precedence_constraint95
FOLLOW_three_param_predicate_in_constraint189
FOLLOW_two_param_predicate_in_constraint183
FREEMARKEREXCEPTION=70
abstractStr.
accession.
accession.
accession.
active.
active.
active.
active.
active.
active.
active.
adapters.
adapterSpec.
addedSurcharge.
adhoctagset.
agent.
algorithm.
algorithm.
algorithm.
algorithm.
alias.
alias.
alias.
alias.
aligners.
aligners.
aligners.
aligners.
aligners.
aligners.
allItems.
anonymizedName.
arguments.
attribute.
attributes.
attributes.
attributes.
backendTimestamp.
barcode.
baseCaller.
baseCoord.
baseDir.
baseIniFile.
baseQualities.
batch_size.
binSize.
binSize.
blockCount.
blockSizes.
blockStarts.
cacheSize.
calledBase.
calledBaseCount.
calledBaseCountForward.
calledBaseCountReverse.
callOne.
callTwo.
centerName.
centerName.
centerProjectName.
children.
children.
childrenUrls.
childSample.
childSample.
childSample.
childSample.
childSample.
classesDir.
clientNotes.
code.
code.
codingStart.
codingStop.
colorMatrix.
colorMatrix.
colorMatrixCode.
colorMatrixCode.
command.
command.
command.
completed.
computeReq.
configPath.
configuration.
configuration.
confirmEmailAddress.
confirmPassword.
connectionString.
consensusAveSeqQuality.
consensusBase.
consensusCallQuality.
consensusMaxSeqQuality.
constructionProtocol.
contig.
contig.
contig.
contig.
count.
countFile.
coverage.
coverage.
created.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimeStamp.
createTimeStamp.
createTstmp.
createTstmp.
createTstmp.
createTstmp.
createTstmp.
criteria.
currentWorkingDir.
cursor.
cursor.
cwd.
cycleCoord.
cycleCount.
cycleCount.
cycleDescriptor.
cycleDescriptor.
cycleDescriptor.
cycles.
cycles.
cycleSequence.
cycleSequence.
data.
database.
dax.
daysUntilDue.
db.
db.
db.
db.
db.
db.
dbmd.
decodeMethod.
defaultValue.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
directoriesNumber.
display.
displayName.
displayName.
displayName.
displayName.
displayValue.
domainObject.
domainObject.
email.
emailAddress.
end.
endDate.
endPage.
entityUrl.
error.
errorCount.
existingType.
existingTypeInt.
exitStatus.
exitStatus.
expectedBaseCall.
expectedNumberReads.
expectedNumberRuns.
expectedNumberSpots.
expectedNumReads.
expectedNumRuns.
expectedNumSpots.
expenseId.
expenses.
expenseType.
experiment.
experiment.
experiment.
experiment.
experiment.
experiment.
experimentAttributeId.
experimentAttributes.
experimentId.
experimentLibraryDesign.
experimentLibraryDesignId.
experimentLibraryDesignService.
experimentLinkId.
experimentLinks.
experiments.
experiments.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentSpotDesign.
experimentSpotDesign.
experimentSpotDesignId.
experimentSpotDesignReadSpecId.
experimentSpotDesignReadSpecService.
experimentSpotDesignService.
expLibDesignDesc.
expLibDesignName.
expLibDesignProtocol.
expLibDesignSelection.
expLibDesignSource.
expLibDesignStrategy.
expSpotDesignAdapterSpec.
expSpotDesignReadsPerSpot.
expSpotDesignTagSpec.
extension.
externalId.
failed.
fastqConvNum.
fastqConvNum.
feature.
featureSetID.
file.
file.
file.
file.
file.
fileAttributeId.
fileAttributes.
fileAttributeService.
fileId.
fileMetaType.
fileMetaType.
fileOne.
filePath.
filePath.
filePath.
filePath.
filePath.
filePath.
files.
files.
files.
files.
files_url.
filesArray.
fileService.
fileService.
fileService.
fileService.
fileService.
fileService.
fileService.
fileService.
fileService.
fileService.
fileService.
fileService.
fileService.
fileService.
fileService.
filesNumber.
fileTwo.
fileTwoURL.
fileType.
fileType.
fileType.
fileTypeId.
fileTypeId.
fileTypeId.
fileTypeService.
fileTypeService.
fileTypeService.
fileTypeService.
fileTypeService.
fileTypeService.
fileUploadService.
fileURL.
fileURL.
finishedTimestamp.
firstName.
firstName.
flowCount.
flowCount.
flowSequence.
flowSequence.
folderStore.
folderStore.
frame.
friendlyRowKey.
fuzzyStartPositionMax.
fuzzyStopPositionMin.
geneChr.
geneId.
geneId.
genomeId.
genomicSequence.
group.
host.
host.
host.
html.
html.
html.
id.
id.
id.
id.
id.
id.
id.
id.
id.
id.
identitySamples.
individualName.
info.
iniFile.
input.
input.
inputAlgorithm.
inputFiles.
institution.
institution.
instrumentModel.
instrumentName.
instrumentName.
invitationCode.
invoice.
invoiceId.
invoiceService.
invoiceService.
isEnd.
isHasFile.
isHasFile.
isHasFile.
isHasFile.
isHasFile.
isHasFile.
isHasFile.
isInvitationCode.
isSelected.
isSelected.
isSelected.
isSelected.
isSelected.
isSelected.
isSelected.
isSelected.
isStart.
itemRgb.
ius.
ius.
ius.
ius.
ius.
ius.
ius.
ius.
ius.
ius.
iusAttributeId.
iusAttributes.
iusId.
iusLinkId.
iusLinks.
iusService.
iusService.
iusService.
iusService.
iusService.
iusService.
iusService.
iusService.
iusService.
iusService.
iusService.
joinDevelopersMailingList.
joinUsersMailingList.
key.
key.
key.
key.
keyIndex.
keyvalues.
label.
label.
label.
label.
label.
label.
label.
label.
label.
label.
label.
lane.
lane.
lane.
lane.
lane.
lane.
lane.
lane.
lane.
lane1.
lane2.
lane3.
lane4.
lane5.
lane6.
lane7.
lane8.
lane_url.
laneAttributeId.
laneAttributes.
laneCount.
laneId.
laneIndex.
laneLinkId.
laneLinks.
lanes.
lanes.
lanes.
lanes.
lanes.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
lastName.
lastName.
layout.
length.
libraryId.
librarySamples.
librarySelectionId.
librarySelectionService.
librarySelectionService.
libraryService.
librarySourceId.
librarySourceService.
librarySourceService.
libraryStrategyId.
libraryStrategyService.
libraryStrategyService.
libraryType.
map.
maxCoverage.
maxCoverage.
maxCoverage.
maximumMappingQuality.
maxLockers.
maxLockObjects.
maxLocks.
md5sum.
md5sum.
memReq.
metadata.
metadata.
metaType.
metaType.
metaType.
minCoverage.
minCoverage.
minCoverage.
minObservations.
minObservationsPerStrand.
minPercent.
minSnpQuality.
minSnpQuality.
minSNVPhred.
mismatchAAChangeBlosumScore.
mismatchAminoAcidChange.
mismatchChr.
mismatchCodonChange.
mismatchCodonPosition.
mismatches.
mismatches.
mismatchId.
mismatchStart.
mismatchStop.
mismatchType.
moduleType.
mutatedGenomicSequence.
mutatedTranslatedSequence.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
nameNode.
ncbiTaxId.
ncbiTaxonomyId.
networkReq.
newType.
nominalLength.
nominalSdev.
notes.
notRunned.
offspringProcessings.
organism.
organism.
organism.
organismId.
organismId.
organismService.
organismService.
originalFileName.
output.
outputDir.
outputFilename.
outputFilename.
outputFiles.
owner.
owner.
owner.
owner.
owner.
owner.
owner.
owner.
owner.
owner.
owner.
owner.
owner.
ownerId.
page.
paidAmount.
pairedEnd.
pairedEnd.
pairedFilePath.
pairedFilePath.
pairedOrientation.
parameters.
parameters.
parameters.
params.
parentProcessingAccession.
parentProcessings.
parents.
parents.
parentUrls.
password.
password.
passwordHint.
pathToFirstFile.
pathToSecondFile.
pending.
permanentBundleLocation.
permBundleLocation.
platform.
platform.
platform.
platformId.
platformInt.
platformInt.
platformService.
platformService.
platformService.
platformService.
platformService.
pmi.
pmi.
postgresqlPersistenceStrategy.
pricePerUnit.
pricePerUnit.
process.
processedCount.
processExitStatus.
processExitStatus.
processing.
processing.
processing.
processing.
processing.
processing.
processing.
processing.
processing.
processingAccession.
processingAttributeId.
processingAttributes.
processingByChildId.
processingByParentId.
processingCount.
processingExperimentsId.
processingExperimentsService.
processingId.
processingIusId.
processingIusService.
processingLaneService.
processingLanesId.
processingRelationshipId.
processingRelationshipService.
processings.
processings.
processings.
processings.
processings.
processings.
processings.
processings.
processings.
processingSamplesId.
processingSamplesService.
processingSequencerRunService.
processingSequencerRunsId.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingStudiesId.
processingStudiesService.
projectId.
projectId.
qualityMultiplier.
qualityNumberOfLevels.
qualityScorer.
qualityType.
readBases.
readClass.
readCount.
reader.
readIndex.
readLabel.
readSpec.
readSpecs.
readsPerSpot.
readsSupportingCallOne.
readsSupportingCallThree.
readsSupportingCallTwo.
readType.
readyToProcess.
referenceAveSeqQuality.
referenceBase.
referenceCallQuality.
referenceId.
referenceMaxSeqQuality.
referenceName.
refLane.
refLane.
regions.
regions.
registration.
registration.
registration.
registration.
registration.
registration.
registration.
registrationId.
registrationService.
registrationService.
registrationService.
registrationService.
registrationService.
registrationService.
registrationService.
registrationService.
relationship.
relativeLocation.
returnValue.
returnValue.
returnValues.
rootSample.
rowId.
rowId.
rows.
runCenter.
runCenter.
runStartTimestamp.
runStartTstmp.
runStopTimestamp.
runStopTstmp.
sample.
sample.
sample.
sample.
sample.
sample.
sample.
sample.
sample.
sample.
sample.
sample_url.
sampleAttributeId.
sampleAttributes.
sampleCode.
sampleId.
sampleId.
sampleId.
sampleLinkId.
sampleLinks.
sampleReportService.
samples.
samples.
samples.
samples.
sampleSearch.
sampleSearchAttributeId.
sampleSearchAttributes.
sampleSearchId.
sampleSearchService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleType.
sampleUrl.
score.
selection.
sender.
sequencer_run_url.
sequencerRun.
sequencerRun.
sequencerRun.
sequencerRun.
sequencerRun.
sequencerRunAttributeId.
sequencerRunAttributes.
sequencerRunId.
sequencerRunId.
sequencerRuns.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunValidator.
sequencerRunWizardValidator.
sequencers.
sequencers.
sequencers.
sequencers.
sequencers.
sequencers.
sequenceSpace.
seqwareRevision.
seqwareVersion.
serialVersionUID.
serialVersionUID.
serialVersionUID.
serialVersionUID.
serialVersionUID.
serialVersionUID.
serialVersionUID.
serialVersionUID.
serialVersionUID.
serialVersionUID.
serialVersionUID.
serialVersionUID.
server.
sessionFactory.
settings.
settings.
settings.
sharedStudies.
sharedWorkflowRuns.
shareExperimentId.
shareFileId.
shareLaneId.
shareProcessingId.
shareSampleId.
shareStudyId.
shareStudyService.
shareStudyService.
shareWorkflowRunId.
shareWorkflowRunService.
shareWorkflowRunService.
site.
size.
size.
skip.
skip.
skip.
skip.
skip.
skipTxt.
slideOneFilePath.
slideOneFilePath.
slideOneLaneCount.
slideOneLaneCount.
slideTwoFilePath.
slideTwoFilePath.
slideTwoLaneCount.
slideTwoLaneCount.
sortKeySample.
source.
source.
spotDesignReadSpec.
sql.
start.
startDate.
startPage.
startPosition.
startPosition.
startPosition.
state.
stats.
status.
status.
status.
status.
status.
status.
status.
status.
statusCmd.
statusCounts.
statuses.
stderr.
stdErr.
stderr.
stdout.
stdOut.
stdout.
stop.
stopPosition.
stopPosition.
stopPosition.
store.
store.
store.
storeType.
strand.
strand.
strategy.
strExpectedNumberReads.
strExpectedNumberRuns.
strExpectedNumReads.
strExpectedNumRuns.
strLaneCount.
strRefLane.
strStartURL.
strStartURL.
studies.
study.
study.
study.
study.
study.
study.
study.
studyAttributeId.
studyAttributes.
studyDAO.
studyId.
studyId.
studyLinkId.
studyLinks.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyTypeDAO.
studyTypeId.
studyTypeService.
studyTypeService.
subjectEmail.
sum.
summaryLines.
svType.
swa.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
tag.
tag.
tag.
tag.
tag.
tags.
tags.
tags.
tags.
tagSetIDs.
tagSpec.
template.
template.
templateEmail.
templateFile.
templatePath.
templateType.
testCmd.
thickEnd.
thickStart.
timeTaken.
tissSource.
title.
title.
title.
tokenNames.
total.
totalPrice.
totalPrice.
totalUnits.
transcriptId.
translatedSequence.
translocationDestinationContig.
translocationDestinationStartPosition.
translocationDestinationStopPosition.
translocationType.
type.
type.
type.
type.
type.
type.
type.
type.
typeNode.
unit.
units.
units.
units.
units.
units.
units.
units.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimeStamp.
updateTimeStamp.
updateTstmp.
updateTstmp.
updateTstmp.
updateTstmp.
updateTstmp.
updateValidator.
url.
url.
url.
url.
url.
url.
url.
url.
url.
url.
url.
url.
url.
url.
url.
url.
url.
url.
url.
url.
urlLabel.
urlLabel.
urlLabel.
urlString.
useIparIntensities.
useIparIntensities.
useOneURL.
username.
userName.
username.
useTwoURL.
useURL.
validationReportService.
validator.
validator.
validator.
validator.
validator.
validator.
validator.
validator.
validator.
validator.
validator.
validator.
validator.
validator.
value.
value.
value.
value.
value.
value.
value.
value.
value.
value.
values.
version.
version.
version.
version.
visibleParams.
wfRuns.
workerName.
workerName.
workflow.
workflow.
workflow.
workflow.
workflowAccession.
workflowAttributeId.
workflowAttributes.
workflowDir.
workflowId.
workflowParam.
workflowParamId.
workflowParamId.
workflowParams.
workflowParamService.
workflowParamService.
workflowParamService.
workflowParamService.
workflowParamValueId.
workflowParamValueService.
workflowParamValueService.
workflowParamValueService.
workflowRun.
workflowRun.
workflowRun.
workflowRun.
workflowRun.
workflowRunAttributeId.
workflowRunAttributes.
workflowRunByAncestorWorkflowRunId.
workflowRunId.
workflowRunId.
workflowRunId.
workflowRunParams.
workflowRunProcessings.
workflowRuns.
workflowRuns.
workflowRuns.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowService.
workflowService.
workflowService.
workflowService.
workflowService.
workflowService.
workflowService.
workflowService.
workflowService.
workflowService.
workflowService.
workflowService.
workflowService.
workflowService.
zygosity.
GFF3_DELETION="deletion"
GFF3_INSERTION="insertion"
GFF3_SNV="VCF_SNV"
GFF3_UNKNOWN_TYPE="unknown_type"
GT=11
GT=11
GTEQ=12
GTEQ=12
GVF_ALIAS="Alias"
GVF_BREAKPOINT_DETAIL="Breakpoint_detail"
GVF_DBXREF="Dbxref"
GVF_END_RANGE="End_range"
GVF_GENOTYPE="Genotype"
GVF_HEMIZYGOUS="hemizygous"
GVF_HETEROZYGOUS="heterozygous"
GVF_HOMOZYGOUS="homozygous"
GVF_INDIVIDUAL="Individual"
GVF_PHASED="Phased"
GVF_REFERENCE_AA="Reference_aa"
GVF_REFERENCE_CODON="Reference_codon"
GVF_REFERENCE_SEQ="Reference_seq"
GVF_SEQUENCE_CONTEXT="Sequence_context"
GVF_START_RANGE="Start_range"
GVF_TOTAL_READS="Total_reads"
GVF_VARIANT_AA="Variant_aa"
GVF_VARIANT_CODON="Variant_codon"
GVF_VARIANT_EFFECT="Variant_effect"
GVF_VARIANT_FREQ="Variant_freq"
GVF_VARIANT_READS="Variant_reads"
GVF_VARIANT_SEQ="Variant_seq"
GVF_ZYGOSITY="Zygosity"
HEMIZYGOUS=3
HETEROZYGOUS=2
HG_19="hg_19"
HG_19="hg_19"
HOMOZYGOUS=1
ID=13
ID=13
Category.info(Object).
Category.info(Object,Throwable).
INPUT_FILES_PARAM='i'
INSERTION=2
INT=14
INT=14
INT_PARAMETERS="int_parameters"
INVALIDARGUMENT=9
INVALIDFILE=7
INVALIDPARAMETERS=2
INVALIDPLUGIN=120
IUS_ATTRIBUTES="Header.IUS_ATTRIBUTES.getTitle()"
IUS_PREFIX="ius_"
IUS_SWA="Header.IUS_SWA.getTitle()"
IUS_TAG="Header.IUS_TAG.getTitle()"
IUS_TAG_PREFIX="Header.IUS_TAG_PREFIX.getTitle()"
JSON="json"
JSON="json"
KEYVALUE_OUT_PARAM='k'
LANE_ATTRIBUTES="Header.LANE_ATTRIBUTES.getTitle()"
LANE_NAME="Header.LANE_NAME.getTitle()"
LANE_NUM="Header.LANE_NUM.getTitle()"
LANE_PREFIX="seq_"
LANE_SWA="Header.LANE_SWA.getTitle()"
LANE_TAG_PREFIX="Header.LANE_TAG_PREFIX.getTitle()"
LT=15
LT=15
LTEQ=16
LTEQ=16
MAX_BASE=94
maxThreads=Integer.parseInt(EnvUtil.getProperty("maxconnections"))
MAXVERSIONS=1000
METADATAINVALIDIDCHAIN=8
MINUS_STRAND=2
AtomImpl)NAME="ExperimentLibraryDesignService"
NAME="ExperimentService"
NAME="ExperimentSpotDesignReadSpecService"
NAME="ExperimentSpotDesignService"
NAME="fileService"
NAME="FileTypeService"
NAME="FileUploadService"
NAME="invoiceService"
NAME="IUSService"
NAME="laneService"
NAME="LibrarySelectionService"
NAME="LibrarySourceService"
NAME="LibraryStrategyService"
NAME="OrganismService"
NAME="PlatformService"
NAME="processingService"
NAME="projectService"
NAME="registrationService"
NAME="sampleService"
NAME="SequencerRunService"
NAME="shareStudyService"
NAME="shareWorkflowRunService"
NAME="StudyService"
NAME="StudyTypeService"
NAME="workflowParamService"
NAME="WorkflowParamValueService"
NAME="WorkflowRunParamService"
NAME="WorkflowRunService"
NAME="WorkflowService"
NAMED_CONSTANT=17
NAMED_CONSTANT=17
NAMED_FUNCTION=18
NAMED_FUNCTION=18
NAMED_THREE_PARAM_PREDICATE=19
NAMED_THREE_PARAM_PREDICATE=19
NAMED_TWO_PARAM_PREDICATE=20
NAMED_TWO_PARAM_PREDICATE=20
NO_STRAND=0
NOT=21
NOT=21
NOTEQUALS=22
NOTEQUALS=22
NOTIMPLEMENTED=-1
NULL=-99
NULLIZYGOUS=4
NUMBER_THREADS_PARAM='t'
OID=0
OID=0
OID=0
OR=23
OR=23
OUTPUT_FILE_PARAM='o'
OUTPUTFILE_PARAM='o'
PAD=15
PAD=15
PAGE_NUM="page"
PAGE_NUM="page"
PARENT_SAMPLE_ATTRIBUTES="Header.PARENT_SAMPLE_ATTRIBUTES.getTitl"{trunked}
PARENT_SAMPLE_NAME="Header.PARENT_SAMPLE_NAME.getTitle()"
PARENT_SAMPLE_SWA="Header.PARENT_SAMPLE_SWA.getTitle()"
PARENT_SAMPLE_TAG_PREFIX="Header.PARENT_SAMPLE_TAG_PREFIX.getTitl"{trunked}
PENDING="pending"
PENDING="pending"
PENDING="pending"
PERSIST_VERSION_CHAINS=false
PLUS_STRAND=1
PositionSeparator=":"
Poster class.prefix="Analysis"
prefix="AnalysisSet"
prefix="FeatureSet"
prefix="Group"
prefix="Feature"
prefix="Reference"
prefix="ReferenceSet"
prefix="Tag"
prefix="TagSet"
prefix="User"
PROCESSING=100
PROCESSING_ALGO="Header.PROCESSING_ALGO.getTitle()"
PROCESSING_ATTRIBUTES="Header.PROCESSING_ATTRIBUTES.getTitle()"
PROCESSING_DATE="Header.PROCESSING_DATE.getTitle()"
PROCESSING_PREFIX="ae_"
PROCESSING_SWID="Header.PROCESSING_SWID.getTitle()"
PROCESSING_TAG_PREFIX="Header.PROCESSING_TAG_PREFIX.getTitle()"
PROGRAMFAILED=1
QUERY_PARAM_FILE='p'
QUERY_PARAM_STRING='s'
QUEUED=101
REFERENCE_ID_PARAM='r'
RESUBMITTED="resubmitted"
RETURNEDHELPMSG=110
ROWS_PER_PAGE="rp"
ROWS_PER_PAGE="rp"
RUNNERERR=91
RUNNING="running"
RUNNING="running"
RUNNING="running"
RUNNING="running"
RUNTIMEEXCEPTION=6
SAMPLE_ATTRIBUTES="Header.SAMPLE_ATTRIBUTES.getTitle()"
SAMPLE_CHILD="s_child"
SAMPLE_NAME="Header.SAMPLE_NAME.getTitle()"
SAMPLE_PREFIX="sam_"
SAMPLE_SAMPLE="s_sample"
SAMPLE_SWA="Header.SAMPLE_SWA.getTitle()"
SAMPLE_SWID="sw"
SAMPLE_TAG_PREFIX="Header.SAMPLE_TAG_PREFIX.getTitle()"
SEARCH_CASE_SENSITIVE="search.checked"
SECONDARY_INDEX="sIndex.out"
SECONDARY_INDEX_HACK=false
SECONDARY_INDEX_PARAM='x'
SELECTED_FILES="selectedLaunchFiles"
SELECTED_NODES="launchSelectedNodes"
SELECTED_VALUES="selectedWorkflowParamValueId"
SEPARATOR="."
SEPARATOR="::"
SEPARATOR="java.io.File.separator"
SEPARATOR="java.io.File.separator"
SEQ_RUN_ID="seq_run_id"
SEQUENCER_RUN_ATTRIBUTES="Header.SEQUENCER_RUN_ATTRIBUTES.getTitl"{trunked}
SEQUENCER_RUN_NAME="Header.SEQUENCER_RUN_NAME.getTitle()"
SEQUENCER_RUN_SWA="Header.SEQUENCER_RUN_SWA.getTitle()"
SEQUENCER_RUN_TAG_PREFIX="Header.SEQUENCER_RUN_TAG_PREFIX.getTitl"{trunked}
SEQUENCER_VIEW="redirect:/sequencerRunList.htm"
sequencers="{ Solexa_1G_Genome_Analyzer, Illumina_G"{trunked}
sequencers="{ Solexa_1G_Genome_Analyzer, Illumina_G"{trunked}
sequencers="{ illumina-ga2, solid-3 }"
SEQWARE_SETTINGS_PROPERTY="SEQWARE_SETTINGS"
abstractStr.
accession.
accession.
accession.
active.
active.
active.
active.
active.
active.
active.
adapters.
adapterSpec.
addedSurcharge.
adhoctagset.
agent.
algorithm.
algorithm.
algorithm.
alias.
alias.
alias.
alias.
allItems.
anonymizedName.
attributes.
attributes.
attributes.
backendTimestamp.
barcode.
baseCaller.
baseCoord.
baseDir.
baseIniFile.
baseQualities.
batch_size.
binSize.
binSize.
blockCount.
blockSizes.
blockStarts.
cacheSize.
calledBase.
calledBaseCount.
calledBaseCountForward.
calledBaseCountReverse.
callOne.
callTwo.
centerName.
centerName.
centerProjectName.
children.
children.
childrenUrls.
childSample.
childSample.
childSample.
childSample.
childSample.
classesDir.
clientNotes.
code.
code.
codingStart.
codingStop.
colorMatrix.
colorMatrix.
colorMatrixCode.
colorMatrixCode.
command.
command.
command.
completed.
compressed.
compressed.
computeReq.
configPath.
confirmEmailAddress.
confirmPassword.
connectionString.
consensusAveSeqQuality.
consensusBase.
consensusCallQuality.
consensusMaxSeqQuality.
constructionProtocol.
contig.
contig.
contig.
contig.
count.
countFile.
coverage.
createConsequenceAnnotationDB.
createCoverageDB.
created.
createDbSNPAnnotationDB.
createMismatchDB.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimeStamp.
createTimeStamp.
createTstmp.
createTstmp.
createTstmp.
createTstmp.
createTstmp.
criteria.
currentWorkingDir.
cwd.
cycleCoord.
cycleCount.
cycleCount.
cycleDescriptor.
cycleDescriptor.
cycleDescriptor.
cycles.
cycles.
cycleSequence.
cycleSequence.
data.
database.
dax.
daysUntilDue.
db.
db.
db.
db.
db.
db.
dbmd.
debug.
decodeMethod.
defaultValue.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
display.
displayName.
displayName.
displayName.
displayName.
displayValue.
domainObject.
domainObject.
email.
emailAddress.
end.
endDate.
endPage.
entityUrl.
errorCount.
existingType.
existingTypeInt.
exitCode.
exitStatus.
exitStatus.
expectedBaseCall.
expectedNumberReads.
expectedNumberRuns.
expectedNumberSpots.
expectedNumReads.
expectedNumRuns.
expectedNumSpots.
expenseId.
expenses.
expenseType.
experiment.
experiment.
experiment.
experiment.
experiment.
experiment.
experimentAttributeId.
experimentAttributes.
experimentDAO.
experimentId.
experimentLibraryDesign.
experimentLibraryDesignId.
experimentLibraryDesignService.
experimentLinkId.
experimentLinks.
experiments.
experiments.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentSpotDesign.
experimentSpotDesign.
experimentSpotDesignId.
experimentSpotDesignReadSpecId.
experimentSpotDesignReadSpecService.
experimentSpotDesignService.
expLibDesignDesc.
expLibDesignName.
expLibDesignProtocol.
expLibDesignSelection.
expLibDesignSource.
expLibDesignStrategy.
expSpotDesignAdapterSpec.
expSpotDesignReadsPerSpot.
expSpotDesignTagSpec.
extension.
externalId.
externalSerializationVersion.
failed.
fastqConvNum.
fastqConvNum.
feature.
featureSetID.
file.
file.
file.
file.
file.
fileAttributeId.
fileAttributes.
fileDAO.
fileId.
fileMetaType.
fileMetaType.
fileOne.
filePath.
filePath.
filePath.
filePath.
filePath.
filePath.
fileReportDAO.
fileReportService.
fileReportService.
fileReportService.
files.
files.
files.
files.
files_url.
filesArray.
fileService.
fileService.
fileService.
fileService.
fileService.
fileService.
fileService.
fileService.
fileService.
fileService.
fileService.
fileService.
fileService.
fileService.
fileService.
fileService.
fileService.
fileTwo.
fileTwoURL.
fileType.
fileType.
fileType.
fileTypeDAO.
fileTypeId.
fileTypeId.
fileTypeId.
fileTypeService.
fileTypeService.
fileTypeService.
fileTypeService.
fileTypeService.
fileTypeService.
fileUploadService.
fileURL.
fileURL.
finalized.
finishedTimestamp.
firstName.
firstName.
flowCount.
flowCount.
flowSequence.
flowSequence.
folderStore.
folderStore.
frame.
friendlyRowKey.
friendlyRowKey.
fullyPaid.
fuzzyStartPositionMax.
fuzzyStopPositionMin.
geneChr.
geneId.
geneId.
genomeId.
genomicSequence.
group.
host.
host.
host.
html.
html.
html.
id.
id.
id.
id.
id.
id.
id.
identitySamples.
includeCoverage.
includeCoverage.
includeIndels.
includeIndels.
includeIndels.
includeSNV.
includeSNV.
includeSNVs.
individualName.
info.
iniFile.
input.
input.
inputAlgorithm.
inputFiles.
institution.
institution.
instrumentModel.
instrumentName.
instrumentName.
invitationCode.
invoice.
invoiceId.
invoiceService.
invoiceService.
isEnd.
isHasFile.
isHasFile.
isHasFile.
isHasFile.
isHasFile.
isHasFile.
isHasFile.
isSelected.
isSelected.
isSelected.
isSelected.
isSelected.
isSelected.
isSelected.
isSelected.
isStart.
itemRgb.
ius.
ius.
ius.
ius.
ius.
ius.
ius.
ius.
iusAttributeId.
iusAttributes.
iusId.
iusLinkId.
iusLinks.
iusService.
iusService.
iusService.
iusService.
iusService.
iusService.
iusService.
iusService.
iusService.
iusService.
iusService.
jdbcTemplate.
joinDevelopersMailingList.
joinUsersMailingList.
key.
key.
key.
key.
keyIndex.
keyvalues.
label.
label.
label.
label.
label.
label.
label.
label.
label.
label.
label.
lane.
lane.
lane.
lane.
lane.
lane.
lane.
lane.
lane1.
lane2.
lane3.
lane4.
lane5.
lane6.
lane7.
lane8.
lane_url.
laneAttributeId.
laneAttributes.
laneCount.
laneDAO.
laneId.
laneIndex.
laneLinkId.
laneLinks.
lanes.
lanes.
lanes.
lanes.
lanes.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
lastName.
lastName.
layout.
length.
libraryId.
librarySamples.
librarySelectionId.
librarySelectionService.
librarySelectionService.
libraryService.
librarySourceId.
librarySourceService.
librarySourceService.
libraryStrategyId.
libraryStrategyService.
libraryStrategyService.
libraryType.
maxCoverage.
maxCoverage.
maxCoverage.
maximumMappingQuality.
maximumMappingQuality.
maxLockers.
maxLockObjects.
maxLocks.
md5sum.
md5sum.
memReq.
metadata.
metadata.
metaType.
metaType.
metaType.
minCoverage.
minCoverage.
minCoverage.
minObservations.
minObservationsPerStrand.
minPercent.
minSnpQuality.
minSnpQuality.
minSNVPhred.
mismatchAAChangeBlosumScore.
mismatchAminoAcidChange.
mismatchChr.
mismatchCodonChange.
mismatchCodonPosition.
mismatchId.
mismatchStart.
mismatchStop.
mismatchType.
moduleParameter.
mutatedGenomicSequence.
mutatedTranslatedSequence.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
nameNode.
ncbiTaxId.
ncbiTaxonomyId.
networkReq.
newType.
nominalLength.
nominalSdev.
notes.
notRunned.
offspringProcessings.
organism.
organism.
organism.
organismId.
organismId.
organismService.
organismService.
originalFileName.
outputDir.
outputFilename.
outputFilename.
outputFiles.
owner.
owner.
owner.
owner.
owner.
owner.
owner.
owner.
owner.
owner.
owner.
owner.
owner.
ownerId.
page.
paidAmount.
pairedEnd.
pairedEnd.
pairedFilePath.
pairedFilePath.
pairedOrientation.
parameters.
parameters.
params.
parentProcessingAccession.
parentProcessings.
parents.
parents.
parentUrls.
password.
password.
passwordHint.
pathToFirstFile.
pathToSecondFile.
payee.
pending.
permanentBundleLocation.
permBundleLocation.
platform.
platform.
platform.
platformId.
platformInt.
platformInt.
platformService.
platformService.
platformService.
platformService.
platformService.
pmi.
pmi.
postgresqlPersistenceStrategy.
pricePerUnit.
process.
processedCount.
processExitStatus.
processExitStatus.
processing.
processing.
processing.
processing.
processing.
processing.
processing.
processing.
processing.
processingAccession.
processingAttributeId.
processingAttributes.
processingByChildId.
processingByParentId.
processingCount.
processingDAO.
processingDAO.
processingExperimentsId.
processingExperimentsService.
processingId.
processingIusId.
processingIusService.
processingLaneService.
processingLanesId.
processingRelationshipId.
processingRelationshipService.
processings.
processings.
processings.
processings.
processings.
processings.
processings.
processings.
processings.
processingSamplesId.
processingSamplesService.
processingSequencerRunService.
processingSequencerRunsId.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingStudiesId.
processingStudiesService.
projectId.
projectId.
qualityMultiplier.
qualityNumberOfLevels.
qualityScorer.
qualityType.
readBases.
readClass.
readCount.
reader.
readIndex.
readLabel.
readOnly.
readSpec.
readSpecs.
readsPerSpot.
readsSupportingCallOne.
readsSupportingCallThree.
readsSupportingCallTwo.
readType.
readyToProcess.
referenceAveSeqQuality.
referenceBase.
referenceCallQuality.
referenceId.
referenceMaxSeqQuality.
refLane.
refLane.
regions.
regions.
registration.
registration.
registration.
registration.
registration.
registration.
registration.
registrationId.
registrationService.
registrationService.
registrationService.
registrationService.
registrationService.
registrationService.
registrationService.
registrationService.
registrationService.
registrationService.
registrationService.
relationship.
relativeLocation.
requireFiles.
returnIds.
returnValue.
returnValue.
rootSample.
rowId.
rowId.
rows.
runCenter.
runCenter.
runStartTimestamp.
runStartTstmp.
runStopTimestamp.
runStopTstmp.
sample.
sample.
sample.
sample.
sample.
sample.
sample.
sample.
sample.
sample.
sample.
sample_url.
sampleAttributeId.
sampleAttributes.
sampleCode.
sampleDAO.
sampleId.
sampleId.
sampleId.
sampleLinkId.
sampleLinks.
sampleReportDAO.
sampleReportService.
sampleReportService.
sampleReportService.
sampleReportService.
samples.
samples.
samples.
samples.
sampleSearch.
sampleSearchAttributeId.
sampleSearchAttributes.
sampleSearchId.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleType.
sampleUrl.
score.
selection.
sender.
sequencer_run_url.
sequencerRun.
sequencerRun.
sequencerRun.
sequencerRun.
sequencerRunAttributeId.
sequencerRunAttributes.
sequencerRunDAO.
sequencerRunId.
sequencerRunId.
sequencerRuns.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunValidator.
sequencerRunWizardValidator.
sequenceSpace.
seqwareRevision.
seqwareVersion.
server.
sessionFactory.
sharedStudies.
sharedWorkflowRuns.
shareExperimentId.
shareFileId.
shareLaneId.
shareProcessingId.
shareSampleId.
shareStudyId.
shareStudyService.
shareStudyService.
shareWorkflowRunId.
shareWorkflowRunService.
shareWorkflowRunService.
site.
size.
size.
skip.
skip.
skip.
skip.
skip.
skipTxt.
slideOneFilePath.
slideOneFilePath.
slideOneLaneCount.
slideOneLaneCount.
slideTwoFilePath.
slideTwoFilePath.
slideTwoLaneCount.
slideTwoLaneCount.
sortKeySample.
source.
source.
spotDesignReadSpec.
sql.
start.
startDate.
startPage.
startPosition.
startPosition.
startPosition.
state.
stats.
status.
status.
status.
status.
status.
status.
status.
status.
statusCmd.
statusCounts.
statuses.
stderr.
stdErr.
stderr.
stdout.
stdOut.
stdout.
stdoutFile.
stop.
stopPosition.
stopPosition.
stopPosition.
store.
store.
store.
storeType.
strand.
strand.
strategy.
strExpectedNumberReads.
strExpectedNumberRuns.
strExpectedNumReads.
strExpectedNumRuns.
strLaneCount.
strRefLane.
strStartURL.
strStartURL.
studies.
study.
study.
study.
study.
study.
study.
study.
studyAttributeId.
studyAttributes.
studyDAO.
studyId.
studyId.
studyLinkId.
studyLinks.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyTypeDAO.
studyTypeId.
studyTypeService.
studyTypeService.
sum.
summaryLines.
svType.
swa.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
tag.
tag.
tag.
tag.
tags.
tags.
tagSetIDs.
tagSpec.
taskGroup.
template.
template.
templateFile.
templatePath.
templateType.
testCmd.
thickEnd.
thickStart.
timeTaken.
SETTINGSFILENOTFOUND=13
tissSource.
title.
title.
title.
total.
totalPrice.
totalUnits.
transcriptId.
translatedSequence.
translocationDestinationContig.
translocationDestinationStartPosition.
translocationDestinationStopPosition.
translocationType.
type.
type.
type.
type.
type.
type.
type.
type.
typeNode.
unit.
units.
units.
units.
units.
units.
units.
units.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimeStamp.
updateTimeStamp.
updateTstmp.
updateTstmp.
updateTstmp.
updateTstmp.
updateTstmp.
updateValidator.
url.
url.
url.
url.
url.
url.
url.
url.
url.
url.
url.
url.
url.
url.
url.
url.
url.
url.
url.
url.
urlLabel.
urlLabel.
urlLabel.
urlString.
useIparIntensities.
useIparIntensities.
useOneURL.
username.
userName.
username.
useTwoURL.
useURL.
uuid.
validationReportService.
validator.
validator.
validator.
validator.
validator.
validator.
validator.
validator.
validator.
validator.
validator.
validator.
validator.
validator.
value.
value.
value.
value.
value.
value.
value.
value.
value.
values.
version.
version.
version.
version.
visibleParams.
wfRuns.
workerName.
workerName.
workflow.
workflow.
workflow.
workflow.
workflowAccession.
workflowAttributes.
workflowDir.
workflowId.
workflowParam.
workflowParamId.
workflowParamId.
workflowParams.
workflowParamService.
workflowParamService.
workflowParamService.
workflowParamService.
workflowParamValueId.
workflowParamValueService.
workflowParamValueService.
workflowParamValueService.
workflowRun.
workflowRun.
workflowRun.
workflowRun.
workflowRun.
workflowRunAttributes.
workflowRunByAncestorWorkflowRunId.
workflowRunId.
workflowRunId.
workflowRunId.
workflowRunParamDAO.
workflowRunParams.
workflowRunProcessings.
workflowRuns.
workflowRuns.
workflowRuns.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflows.
workflowService.
workflowService.
workflowService.
workflowService.
workflowService.
workflowService.
workflowService.
workflowService.
workflowService.
workflowService.
workflowService.
workflowService.
workflowService.
workflowService.
workflowService.
workflowService.
zygosity.
SIZE_COUNT_FILE=5
SIZE_COUNT_TREE=20
SNV=1
Syntax:
./SNVMix2 -m [-i ] [-o ] [-T | -C | -F] [-p < q | m | s >] [-t < mb | m | b | M | Mb | MB | SNVMix1>] [-q <#>] [-Q <#>] [-a/-b/-d <#,#,#>] [-M ] [-h]
Required:
-m model file, a line for mu and a line for pi, three
space-separated values each, like:
mu 0.xxxxxxxx 0.xxxxxxxx 0.xxxxxxxx
pi 0.xxxxxxxx 0.xxxxxxxx 0.xxxxxxxx
Optional:
-i quality pileup, from pileup2matlab.pl script (def: STDIN)
-o where to put the results (def: STDOUT)
-T | -C | -F Train, Classify or Filter (def: Classify)
-p q|m|s Input pileup format (def: s)
q = quality
m = MAQ
s = SAMtools
-t mb|m|b|M|Mb|MB|SNVMix1
Filter type (def: mb)
mb Lowest between map and base quality
m Filter on map, and use as surrogate for base quality
b Filter on base quality, take map quality as 1
M Filter on map quality but use only base quality
Mb Filter on map quality and use both map and base qualities
MB Filter on map quality AND base quality
SNVMix1 Filter on base quality and map quality, afterwards consider them perfect
-q # Cutoff Phred value for Base Quality, anything <= this value is ignored (def: Q19)
-Q # Cutoff Phred value for Map Quality, anything <= this value is ignored (def: Q19)
Training parameters:
-a #,#,# Provide alpha training parameters
-b #,#,# Provide beta training parameters
-d #,#,# Provide delta training parameters
-M Provide a file containing training parameters (will override -a, -b and -d)
Values are space-separated:
alpha # # #
beta # # #
delta # # #
-apply-filter
-perl-path Path to perl installation
-filter-path Path to the filter script
-threshold THRESHOLD is given, then SNVs will be reported when the selected probability exceeds this
-c [2|3] TYPE is the number of classes to consider
'2' considers only AA and {AB U BB} (default)
'3' considers AA, AB and BB
-h this message
SORT_NAME="sortname"
SORT_NAME="sortname"
SORT_NAME="sortname"
SORT_ORDER="sortorder"
SORT_ORDER="sortorder"
SORT_ORDER="sortorder"
SORT_ORDER_ASC="asc"
SORT_ORDER_ASC="asc"
SORT_ORDER_DESC="desc"
SORT_ORDER_DESC="desc"
SQLQUERYFAILED=82
START_ALL_QUERYDATELONG="start-ALL_query-date-long"
START_PMC_QUERYDATELONG="start-PMC_query-date-long"
START_PMCSI_QUERYDATELONG="start-PMCSI_query-date-long"
START_QUAL_QUERYDATELONG="start-QUAL_query-date-long"
STARTCOUNTDATELONG="start-count-date-long"
STARTDUMP_QUERYDATELONG="start-dump_query-date-long"
STDOUTERR=90
STRING=24
STRING=24
STRINGID=20
STUDY_ATTRIBUTES="Header.STUDY_ATTRIBUTES.getTitle()"
STUDY_ID="study_id"
STUDY_ID="study_id"
STUDY_PREFIX="study_"
STUDY_SWA="Header.STUDY_SWA.getTitle()"
STUDY_TAG_PREFIX="Header.STUDY_TAG_PREFIX.getTitle()"
STUDY_TITLE="Header.STUDY_TITLE.getTitle()"
STUDY_VIEW="redirect:/myStudyList.htm"
SUBMITTED="submitted"
SUCCESS="success"
SUCCESS=0
SUCCESS="success"
SUCCESS="success"
SV=4
SV_COMPLEX=1
SV_DELETION=2
SV_DELETION_AND_INVERSION=3
SV_DISPERSED_DUPLICATION=4
SV_DUPLICATION_AND_INVERSION=5
SV_INVERSION=6
SV_LOCATION_DOWNSTREAM=2
SV_LOCATION_UNKNOWN=0
SV_LOCATION_UPSTREAM=1
SV_TANDEM_DUPLICATION=7
SV_UNKNOWN=0
T__26=26
T__26=26
TABLE_MODEL="tablemodel"
TABLE_MODEL="tablemodel"
TABLE_SEL="tablesel"
TABLE_SEL="tablesel"
TAG=10
TAG_CHAR='n'
TAGSETS_PARAM='s'
TEST_TABLE_PREFIX="Constants.Term.NAMESPACE.getTermValue(S"{trunked}
tokenNames="new String[] {, , ,"{trunked}
Category.debug(Object).
Category.debug(Object,Throwable).
TRANSLOCATION=5
TRANSLOCATION_COMPLEX=3
TRANSLOCATION_INTERCHR=2
TRANSLOCATION_INTRACHR=1
TRANSLOCATION_UNKNOWN=0
TYPE_TREE="sr"
TYPE_TREE="st"
TYPE_TREE_COMPLETED="wfr"
TYPE_TREE_RUNNNING="wfrr"
Unclassified=1
UNKNOWN="unknown"
UNKNOWN_TYPE=0
UNKNOWN_ZYGOSITY=0
VALUE_SEPARATOR_PARAM=','
VARIENT=0
VCF="VCFVariantImportWorker.VCF"
VCF="VCF"
VCF_CALLED_BASE="call_base"
VCF_CONSENSUS_BASE="con_base"
VCF_FILTER="filter"
VCF_HETEROZYGOUS="heterozygous"
VCF_HOMOZYGOUS="homozygous"
VCF_INFO="info"
VCF_READ_COUNTS="read_count"
VCF_REFERENCE_BASE="ref_base"
VCF_SECOND_ID="id"
VCF_SNV="SNV"
VERSION="0.7.0"
Category.warn(Object).
Category.warn(Object,Throwable).
WHITESPACE=25
WHITESPACE=25
WORKER_CHAR_PARAM='w'
WORKFLOW_NAME="Header.WORKFLOW_NAME.getTitle()"
WORKFLOW_RUN_NAME="Header.WORKFLOW_RUN_NAME.getTitle()"
WORKFLOW_RUN_PREFIX="wfr_"
WORKFLOW_RUN_STATUS="Header.WORKFLOW_RUN_STATUS.getTitle()"
WORKFLOW_RUN_SWA="Header.WORKFLOW_RUN_SWA.getTitle()"
WORKFLOW_SWA="Header.WORKFLOW_SWA.getTitle()"
WORKFLOW_VERSION="Header.WORKFLOW_VERSION.getTitle()"
|
||||||||||
| PREV NEXT | FRAMES NO FRAMES | |||||||||